In blast-induced traumatic brain injury, shock waves (SW) play an important role along with cavitation phenomena. Due to the lack of reliable and reproducible experimental investigations, we have a limited understanding of the role of cavitation in brain damage. The present study aims to develop an atomistic simulation model to determine the role of shock-induced impulse and different constituents of the brain’s extra-cellular matrix (ECM) on the formation mechanism, stability and collapsing mechanism of nanobubbles in the ECM. The ECM in the brain can be divided into three major types depending on their location behind the blood-brain barrier, namely (a) the basement membrane (basal lamina), (b) the perineuronal nets and (3) the neural interstitial matrix. In this paper, we have studied the interaction of nanobubbles with bio-molecules of the perineuronal nets. We have chosen this zone of the ECM because we are interested to obtain the role of cavitation bubble collapse in neuron damage. Most biomolecules of perineuronal nets are slender in shape and flexible which is believed to induce special solid-fluid interaction between the fluid domain and the solid domain within the ECM. In addition, perineuronal nets contain a significant number of sodium ions. The relationship between sodium ion and solid-like constituents of perineuronal nets on the stability and the collapsing mechanism of nanobubbles will be discussed.